Background: It has been shown that patients with atrial fibrillation have a poor prognosis in the early recovery phase after ischemic stroke (IS) or transient ischemic attack (TIA). The purpose of this study was to identify the risk factors associated with poor outcome, including mortality, 3 months after the onset of IS in patients with atrial fibrillation. Methods: We have prospectively investigated the characteristics of patients selected from the China National Stroke Registry. Poor outcome was defined as the modified Rankin scale score of 3 or more or death at 3-month follow-up. Association between the relevant risk factors and poor outcome was analyzed using logistic regression analysis. Additionally, the interaction between multiple risk factors was also analyzed. Results: Each year of age (odds ratio [OR]: 1.031; 95% confidence interval [CI] 1.017-1.045), the National Institutes of Health Stroke Scale (NIHSS) at admission (OR: 1.219; 95% CI 1.185-1.254), and female gender (OR: 1.710; 95% CI 1.296-2.256) were independent risk factors for poor outcome at 3 months after IS. Independent risk factors for 3-month mortality included age (OR: 1.024; 95% CI 1.007-1.041), NIHSS at admission (OR: 1.122; 95% CI 1.100-1.144), and history of heart failure (OR: 1.855; 95% CI 1.141-3.015). Conversely, heavy alcohol intake was associated with protective effect on mortality poststroke (OR: .400; 95% CI.173-.928). There was no significant interaction between age and gender (for mortality, P = .16; for poor outcomes, P = .91), age and NIHSS (for mortality, P = .38; for poor outcomes, P = .11), and gender and NIHSS (for mortality, P = .33; for poor outcomes, P = .80). Conclusions: Age, gender, and NIHSS score were independently associated with poor outcome for IS or TIA patients with nonvalvular atrial fibrillation in the early recovery stage.